VMD-L Mailing List

From: Dong Luo (us917_at_yahoo.com)
Date: Mon Apr 01 2013 - 10:39:56 CDT

By information on http://www.ks.uiuc.edu/Research/vmd/plugins/cgtools/, I don't see why psf file is required for the AA (all-atoms) model. Only pdb file is used for the conversion. No Charmm or OPLS force field parameter files are needed. But you do need a psf file to run simulations for newly coverted CG molecule. Just follow instructions in the link.

Dong

________________________________
 From: WuChaofu <xiaowu759_at_hotmail.com>
To: "vmd-l_at_ks.uiuc.edu" <vmd-l_at_ks.uiuc.edu>
Sent: Monday, April 1, 2013 3:55 AM
Subject: vmd-l: CGTools with pdb and top files
 

 
Dear VMDers,
I try to use the CGTools plugin to perform the conversion from AA to CG. As confirmed that, both pdb and psf files are required for the AA model. However, I have only a top file in the format of GROMACS instead of a psf file. In the top file, all parameters are described by the OPLSAA force field. How should I perform the conversion with only pdb and top file in hand? Or How should I modify the tool to achieve this? Please give me some hints. Thank you very much!
Chaofu Wu